inst/cli/run_ggVennDiagram.R

In gaospecial/ggVennDiagram: A 'ggplot2' Implement of Venn Diagram

#!/usr/bin/env Rscript
# Copyright 2023-2023 Chun-Hui Gao <gaospecial@gmail.com>
#
#  This file is free software: you may copy, redistribute and/or modify it
#  under the terms of the GNU General Public License as published by the
#  Free Software Foundation, either version 2 of the License, or (at your
#  option) any later version.
#
#  This file is distributed in the hope that it will be useful, but
#  WITHOUT ANY WARRANTY; without even the implied warranty of
#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
#  General Public License for more details.
#
#  You should have received a copy of the GNU General Public License
#  along with this program.  If not, see <http://www.gnu.org/licenses/>.

# This script is a standalone R wrapper that can be used to plot Venn and Upset plot
# using ggVennDiagram. It is for command line interface and can be used to build a
# TBtools plugin.

##### STEPS #####

#### install R - firstly install RServer plugin ####


#### install package ####
if (!requireNamespace("pak", quietly = TRUE)){
  install.packages("pak")
}

if (!requireNamespace("ggVennDiagram", quietly = TRUE)){
  pak::pak("ggVennDiagram")
}

if (!requireNamespace("argparse", quietly = TRUE)){
  pak::pak("argparse")
}

library("ggVennDiagram")
library("argparse")

#### process arguments ####
## see https://docs.python.org/3/library/argparse.html#the-add-argument-method
parser <- ArgumentParser(description='This is a ggVennDiagram wrapper,
                         by which you can instantly create publication quality
                         Venn diagram (no more than 7 sets) and Upset plots
                         (unlimited No. of sets). For example: PROGRAM -s a,b,c b,c,d e,f')
parser$add_argument('--set', '-s', nargs = '+', help='set members. must be comma separated string. at least one set is needed.')
parser$add_argument('--force-upset', default = FALSE, help = 'specifiy the type of plot')
parser$add_argument("--out", "-o", default = "plot.png",help = "specify the output file of plot. filetype (png/jpg/pdf) is determined by its suffix automatically.")
parser$add_argument("--name", default = NULL, help = "specify the names of sets (Set_1, Set_2, ...)")
parser$add_argument("--set-label-color", default = "black", help = 'color of set labels ("black")')
parser$add_argument("--set-label-size", default = "NA", help = "size of set labels (NA)" )
parser$add_argument("--label", choices = c("count","percent","both","none"), help = 'format of region labels')
parser$add_argument("--label-alpha", default = 0.5, help = "set 0 to remove the background of region labels")
parser$add_argument('--label-geom', default = "label", choices = c("label", "text"), help = 'layer of region labels, choose from c("label", "text")')
parser$add_argument('--label-color', default = "black", help = 'color of region labels ("black")')
parser$add_argument('--label-size', default = "NA", help = 'size of region labels (NA)')
parser$add_argument('--label-percent-digit', default = 0, help = 'number of digits when formatting percent label (0)')
parser$add_argument('--label-txt-width', default = 40, help = 'width of text used in showing intersect members, will be ignored unless show_intersection is TRUE (40)')
parser$add_argument('--edge-lty', default = "solid", help = 'line type of set edges ("solid")')
parser$add_argument('--edge-size', default = 1, help = 'line width of set edges (1)')

# parser$print_help()

args = parser$parse_args()
args = lapply(args, function(x) ifelse(x == "NA", NA, x))

list = as.list(args$set)

#### output results ####
## plot a png/jpg/tiff, and can export as both PDF and PPTX
p = ggVennDiagram(list,
                  category.names = args$name,
                  set_color = args$set_label_color,
                  set_size = args$set_label_size,
                  label = args$label,
                  label_alpha = args$label_alpha,
                  label_geom = args$label_geom,
                  label_color = args$label_color,
                  label_size = args$label_size,
                  label_percent_digit = args$label_percent_digit,
                  label_txtWidth = args$label_txt_width,
                  edge_lty = args$edge_lty,
                  edge_size = args$edge_size,
                  force_upset = args$force_upset)
ggplot2::ggsave(args$out, p)